Fig. 5
TET1 KD in human T-ALL cells alters gene expression by changing DNA (hydroxy)methylation. MeDIP-, hMeDIP-, and RNA-seq analysis of human T-ALL cells (CCRF-CEM) before (SCR) and upon TET1 KD (TET1sh). a Genomic distribution of DMRs and hDMRs is displayed as chromosome-based circular plot. Cutoff: log2FC ≥ 1 with a P value of ≤ 10−4. b Hypo- or hypermethylated DMRs and hDMRs are shown annotated for their association with mRNAs, enhancers, super-enhancers, small ncRNAs, and long ncRNAs. c Hypo- or hypermethylated DMRs and hDMRs associated with mRNAs are shown annotated for cis-regulatory elements: CpG islands, exons, introns, 5′-/3′-UTRs, and sequences greater than 2 kbp upstream or downstream of the nearest gene. d RNA-seq analysis: heatmap showing hierarchical clustering of 3302 DEGs. Gene names are listed in Additional file 3. e Gene ontology analysis (DAVID) based on DEGs. f Gene set enrichment analysis (GSEA) of RNA expression associated with biological processes. g Intersection between DMRs, hDMRs, and DEGs. Gene names are listed in Additional file 3. Heatmap showing hierarchical clustering of genes both differentially expressed and differentially (hydroxy)methylated: h DEGs and DMRs and i DEGs and hDMRs